RetrogeneDB ID:

retro_ogar_1835

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873569.1:6586067..6586950(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS2
Ensembl ID:ENSOGAG00000010098
Aliases:None
Description:ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]


Retrocopy-Parental alignment summary:






>retro_ogar_1835
ATGGCAGATGACACTGGTGCAGCAGGAAGGCCTAGAGGCTCTGGGGGCCCCGGAATGGGAAGCCATGGTGGTTTCCGTGG
AGGCTTCAGCAGCGGCATTCATTTGGGCCAGGGTCACAGCTGTGGTGTGGGTTGGGGCTGAGGCCGCAGAGTTCATGGAG
GCAAGGCCAAGGACAAAGAGTCGATGCCTGTCACCAAGCTGGGCCACCTGGTCAAGGACATGAAGATCAATCCCTGGAGG
GAGCTATCTCTTCTCCCTGCCCATTAAGGAATCTGAGATCATTGATTTTTTTTCTTGGGGGCATCTCTCAAGGATGAAGT
TTTGAAGATTATGCCAGTGCAAAAAATAGACCCACACTGGCCAGCGGACCAGGTTCAAGGCATGTGTTGCCATTGGGGAC
TACAATGGCCATGTCGATCTGAGTGTTAAGTGTTCCAAGGAAGTAGCCACTGCCATCTGAGGGGCCATCATCCTGGCCAA
GCTCTCTATTGTCCCAGTGCGGGGAGGCTACTGGGGGAATAAGATCGACAAGCCTTACCCTGTTCCTTGCAAGGTGACAG
GCCACTGTGGCTCTGTGCTGGTAGGTCTCATCCCTGCTCCTAGAGGAACTGGCATTGTCTCAGCGCCTGTGCCTAAGAAG
CTGCTAATGATGACTGGGATCAATGACTGCTACATTTCAGCTAGGGGCTGCACTGCCACCCTGGGCAACTTTGCCAAGGC
CACTTTTGATGCCATTTCCAAGACCTATAGCTATTTCACTCCTGACTTCTGGGAAGACACAGTATTCACCAAGTCTCTTT
ACCAAGAATTCACTGACCATCTTGTCAAGACCCACACCAGAGTCTCTGTGCAGAGGACCCAGGCTCCAGCTGTGGCTACA
ACA

ORF - retro_ogar_1835 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.45 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMADDAGAAGGPGGPGGPGMGGRGGFRGGFGSGIR-GRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRL
MADD.GAAG.P.G.GGPGMG..GGFRGGF.SGI..G.G...G.G.G.GR...GGKA.DKE.MPVTKLG.L
RetrocopyMADDTGAAGRPRGSGGPGMGSHGGFRGGFSSGIHLGQGHSCGVGWG*GRRVHGGKAKDKESMPVTKLGHL
ParentalVKDMKI-KSLEEIYLFSLPIKESEIIDFFLG-ASLKDEVLKIMPVQKQ-TRAGQRTRFKAFVAIGDYNGH
VKDMKI..SLE.......P..........LG.ASLKDEVLKIMPVQK..T..GQRTRFKA.VAIGDYNGH
RetrocopyVKDMKI<QSLEGAISSPCPLRNLRSLXXXLG>ASLKDEVLKIMPVQKI>THTGQRTRFKACVAIGDYNGH
ParentalVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVS
V.L.VKCSKEVATAI.GAIILAKLSIVPVR.GYWGNKI.KP..VPCKVTG.CGSVLV.LIPAPRGTGIVS
RetrocopyVDLSVKCSKEVATAI*GAIILAKLSIVPVRGGYWGNKIDKPYPVPCKVTGHCGSVLVGLIPAPRGTGIVS
ParentalAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKT
APVPKKLLMM.GI.DCY.SARGCTATLGNFAKATFDAISKTYSY.TPD.W..TVFTKS.YQEFTDHLVKT
RetrocopyAPVPKKLLMMTGINDCYISARGCTATLGNFAKATFDAISKTYSYFTPDFWEDTVFTKSLYQEFTDHLVKT
ParentalHTRVSVQRTQAPAVATT
HTRVSVQRTQAPAVATT
RetrocopyHTRVSVQRTQAPAVATT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_1835 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 9 parental genes, and 139 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000025491 retrocopy
retro_acar_57,
Felis catus ENSFCAG000000291916 retrocopies
retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens ENSG0000014098847 retrocopies
retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688, retro_hsap_1722, retro_hsap_1812, retro_hsap_1830, retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Macropus eugenii ENSMEUG000000045082 retrocopies
retro_meug_156, retro_meug_2103,
Microcebus murinus ENSMICG0000001276528 retrocopies
retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica ENSMODG000000160771 retrocopy
retro_mdom_536,
Otolemur garnettii ENSOGAG00000010098 19 retrocopies
retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835 , retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842, retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii ENSSHAG000000152135 retrocopies
retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri ENSTBEG0000000672630 retrocopies
retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,


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